Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Reconstructing the history of variation in effective population size along phylogenies

View ORCID ProfileMathieu Brevet, View ORCID ProfileNicolas Lartillot
doi: https://doi.org/10.1101/793059
Mathieu Brevet
1Station d’écologie théorique et expérimentale UMR 5321, 09200 Moulis, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mathieu Brevet
Nicolas Lartillot
2Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nicolas Lartillot
  • For correspondence: nicolas.lartillot@univ-lyon1.fr
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

The nearly-neutral theory predicts specific relations between effective population size (Ne) and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward, owing to the difficulty in estimating Ne. Here, we introduce an integrative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly-neutral theory and an estimation of the allometric scaling of the ratios of non-synonymous over synonymous polymorphism (πN /πS) and divergence (dN/dS) with respect to Ne. As an illustration, we applied our method to primates, for which the nearly-neutral predictions were mostly verified. Under a purely nearly-neutral model with a constant DFE across species, we find that the variation in πN /πS and dN/dS as a function of Ne is too large to be compatible with current estimates of the DFE based on site frequency spectra. The reconstructed history of Ne shows a ten-fold variation across primates. The mutation rate per generation u, also reconstructed over the tree by the method, varies over a three-fold range and is negatively correlated with Ne. As a result of these opposing trends for Ne and u, variation in πS is intermediate, primarily driven by Ne but substantially influenced by u. Altogether, our integrative framework provides a quantitative assessment of the role of Ne and u in modulating patterns of genetic variation, while giving a synthetic picture of their history over the clade.

Significance statement Natural selection tends to increase the frequency of mutants of higher fitness and to eliminate less fit genetic variants. However, chance events over the life of the individuals in the population are susceptible to introduce deviations from these trends, which are expected to have a stronger impact in smaller populations. In the long-term, these fluctuations, called random drift, can lead to the accumulation of mildly deleterious mutations in the genomes of living species, and for that reason, the effective population size (usually denoted Ne, and which captures the relative strength of drift, relative to selection) has been proposed as a major determinant of the evolution of genome architecture and content. A proper quantitative test of this hypothesis, however, is hampered by the fact that Ne is difficult to estimate in practice. Here, we propose a Bayesian integrative approach for reconstructing the broad-scale variation in Ne across an entire phylogeny, which in turns allows for quantifying how Ne correlates with life history traits and with various measures of genetic diversity and selection strength, between and within species. We apply this approach to the phylogeny of primates, and observe that selection is indeed less efficient in primates characterized by smaller effective population sizes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/bayesiancook/coevol

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted June 06, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Reconstructing the history of variation in effective population size along phylogenies
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Reconstructing the history of variation in effective population size along phylogenies
Mathieu Brevet, Nicolas Lartillot
bioRxiv 793059; doi: https://doi.org/10.1101/793059
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Reconstructing the history of variation in effective population size along phylogenies
Mathieu Brevet, Nicolas Lartillot
bioRxiv 793059; doi: https://doi.org/10.1101/793059

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4383)
  • Biochemistry (9601)
  • Bioengineering (7097)
  • Bioinformatics (24868)
  • Biophysics (12621)
  • Cancer Biology (9959)
  • Cell Biology (14358)
  • Clinical Trials (138)
  • Developmental Biology (7954)
  • Ecology (12110)
  • Epidemiology (2067)
  • Evolutionary Biology (15989)
  • Genetics (10929)
  • Genomics (14745)
  • Immunology (9871)
  • Microbiology (23680)
  • Molecular Biology (9486)
  • Neuroscience (50884)
  • Paleontology (369)
  • Pathology (1540)
  • Pharmacology and Toxicology (2683)
  • Physiology (4019)
  • Plant Biology (8657)
  • Scientific Communication and Education (1510)
  • Synthetic Biology (2397)
  • Systems Biology (6439)
  • Zoology (1346)